|
| Status |
Public on May 07, 2023 |
| Title |
PreIR-NTN_SMG Replicate 5 |
| Sample type |
SRA |
| |
|
| Source name |
Submandibular Gland
|
| Organism |
Mus musculus |
| Characteristics |
strain: CH3
tissue: SMG
age: 1 year old (300 days after treatment)
agent: PreIR-NTN
|
| Treatment protocol |
Injection of AAV2-GFP or Cere-120 10 days before irradiation of the murine SMGs and tissue harvested after 300 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SMGs were harvested, minced and lyzed in RNA lysis buffer and homogenized using Fastprep-24 instrument with lysing matrix D tubes. RNA was purified using RNAqueous-4PCR kit (Ambion, Houston, TX, USA).
Total RNA per sample was reverse transcribed, and full-length cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA). Libraries for Illumina sequencing were prepared using the Nextera XT kit (Illumina), pooled, and analyzed on four lanes of a NextSeq 500 sequencer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PreIR-NTN_5
|
| Data processing |
Basecalls performed using Illumina’s RTA 2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in single-pass mode. With the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.
|
| |
|
| Submission date |
May 08, 2020 |
| Last update date |
May 07, 2023 |
| Contact name |
Matthew P Hoffman |
| E-mail(s) |
mhoffman@dir.nidcr.nih.gov
|
| Phone |
301-496-1660
|
| Organization name |
NIDCR
|
| Lab |
MMS
|
| Street address |
30 Convent Dr MSC4370
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE150112 |
RNA seq analysis of Cere-120 (AAV2-NRTN) pretreatment in irradiated SMGs compared to AAV2-GFP pretreatment and Non-IR controls. |
|
| Relations |
| BioSample |
SAMN14854765 |
| SRA |
SRX8293388 |
